Wish list
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The full text of the PDF is indexed as well, so it would require extracting the notes as well, which is of course possible.
The search (when set to "everything") will search this too. However, it's not very intuitive, as the results don't present the passages from the PDF file. I vaguely remember that this will change in the future.
Feel free to continue discussions of any of these features in their respective dedicated threads.